Abstract Algal-based bioenergy products have faced multiple economic and environmental problems. To counter these problems, algal-based biorefineries have been proposed as a promising solution. Multiple environmental and economic assessments have analyzed this concept. However, a wide variation in results was reported. This study performs a review to evaluate the methodological reasons behind this variation. Based on this review, four main challenges for a sustainability assessment were identified: 1) the use of a clear framework; 2) the adaptation of the methodology to all stages of technological maturity; 3) the use of harmonized assumptions; 4) the integration of the technological process. A generic methodology, based on the integration of a techno-economic assessment methodology and a streamlined life cycle assessment was proposed. This environmental techno-economic assessment can be performed following an iterative approach during each stage of technology development. In this way, crucial technological parameters can be directly identified and evaluated during the maturation of the technology. The use of this assessment methodology can therefore act as guidance to decrease the time-to-market for innovative and sustainable technologies.